I needed to extract all hits from one list (list.txt) which can be found in one of the columns of another (here in Data.txt) into a third (output.txt).
Data.txt (tab delimited)
some_data more_data other_data here yet_more_data etc
A B 2 Gee;Whiz;Hello 13 12
A B 2 Gee;Whizz;Hi 56 32
E 4 Btm;Lol 16 2
T 3 Whizz 13 3
List.txt
Gee
Whiz
Lol
Ideally output.txt looks like
some_data more_data other_data here yet_more_data etc
A B 2 Gee;Whiz;Hello 13 12
A B 2 Gee;Whizz;Hi 56 32
E 4 Btm;Lol 16 2
So I tried a shell script
for ids in List.txt
do
grep $ids Data.txt >> output.txt
done
except I typed out everything (cut and paste actually) in List.txt in said script.
Unfortunately it gave me an output.txt including the last line, I assume as 'Whizz' contains 'Whiz'.
I also tried cat Data.txt | egrep -F "List.txt" and that resulted in grep: conflicting matchers specified -- I suppose that was too naive of me. The actual files: List.txt contains a sorted list of 985 words, Data.txt has 115576 rows with 17 columns.
Some help/guidance would be much appreciated thanks.
Try something like this:
for ids in List.txt
do
grep "[TAB;]$ids[TAB;]" Data.txt >> output.txt
done
But it has two drawbacks:
"Data.txt" is scanned multiple times
You can get one line multiple times.
If it is problem try two step version:
cat List.txt | sed -e "s/.*/[TAB;]\0[TAB;]/g" > List_mod.txt
grep -f List_mod.txt Data.txt > output.txt
Note:
TAB character can be inserted by combination Ctrl-V following by Tab key in command line, and Tab character in editor. You have to check if your edit does not change tab to series of spaces.
The UNIX tool for general text processing is "awk":
awk '
NR==FNR { list[$0]; next }
{
for (word in list) {
if ($0 ~ "[\t;]" word "[\t;]") {
print
next
}
}
}
' List.txt Data.txt > output.txt
Related
I need to merge several files, removing redundant lines among files, while keeping redundant lines within files. A schematic representation of my files is the following:
File1.txt
1
2
3
3
4
5
6
File2.txt
6
7
8
8
9
File3.txt
9
10
10
11
The desired output would be:
1
2
3
3
4
5
6
7
8
8
9
10
10
11
I would prefer to get a solution either in awk, or in bash or in R language. I searched the web for solutions and, though there were plenty of them* (please find some examples below), there were all removing duplicated lines regardless of the fact that they were located within or outside files.
Thanks in advance.
Arturo
Examples of previous solutions removing redundant lines both within and outside files:
https://unix.stackexchange.com/questions/50103/merge-two-lists-while-removing-duplicates
https://unix.stackexchange.com/questions/457320/combine-text-files-and-delete-duplicate-lines
https://unix.stackexchange.com/questions/350520/awk-combine-two-big-files-and-remove-duplicated-lines
https://unix.stackexchange.com/questions/257467/merging-2-files-and-keeping-the-one-duplicate
With your shown samples, could you please try following. This will NOT remove redundant lines within files but will remove them file wise.
awk '
FNR==1{
for(key in current){
total[key]
}
delete current
}
!($0 in total)
{
current[$0]
}
' file1.txt file2.txt file3.txt
Explanation: Adding detailed explanation for above.
awk ' ##Starting awk program from here.
FNR==1{ ##Checking condition if its first line(of each file) then do following.
for(key in current){ ##Traverse through current array here.
total[key] ##placing index of current array into total(for all files) one.
}
delete current ##Deleting current array here.
}
!($0 in total) ##If current line is NOT present in total then do following.
{
current[$0] ##Place current line into current array.
}
' file1.txt file2.txt file3.txt ##Mentioning Input_file names here.
Here's a trick adding on to https://stackoverflow.com/a/15385080/3358272 using diff and its output format. There is likely a presumption of "sorted" here, untested.
out=$(mktemp -p .)
tmpout=$(mktemp -p .)
trap 'rm -f "${out}" "${tmpout}"' EXIT
for F in ${#} ; do
{ cat "${out}" ;
diff --changed-group-format='%>' --unchanged-group-format='' "${out}" "${F}" ;
} > "${tmpout}"
mv "${tmpout}" "${out}"
done
cat "${out}"
Output:
$ ./question.sh F*
1
2
3
3
4
5
6
7
8
8
9
10
10
11
$ diff <(./question.sh F*) Output.txt
(Per markp-fuso's comment, if File3.txt had two 9s, this would preserve both.)
I have two files, file A may be in file B and I would like to count for each line in file A, how many times it occurs in file B. For example:
File A:
GAGGACAGACTACTAAAGCC
CTTGCCGCAGATTATCAGAG
CCAGCTTGATGTGTCCTGTG
TGATAGGCAGTGGAACACTG
File B:
NTCTTGAGGAAAGGACGAATCTGCGGAGGACAGACTACTAAAGCCGTTTGAGAGCTAGAACGAGCAAGTTAAGAGA
TCTTGAGGAAAGGACGAAACTCCGGAGGACAGACTACTAAAGCCGTTTTAGAGCTAGAAAGCGCAAGTTAAACGAC
NTCTTGAGGAAAGGACGAATCTGCGCTTGCCGCAGATTATCAGAGGTATGAGAGCTAGAACGAGCAAGTTAAGAGC
TCTTGAGGAAAGGACGAAAGTGCGCTTGCCGCAGATTATCAGAGGTTTTAGAGCTAGAAAGAGCAAGTTAAAATAA
GATCTAGTGGAAAGGACGATTCTCCGCTTGCCGCAGATTATCAGAGGTTGTAGAGCTAGAACTAGCAAGTGACAAG
ATCTTGAGGAAAGGACGAATCTGCGCTTGCCGCAGATTATCAGAGGTTTGAGAGCTAGAACTAGCAAGTTAATAGA
CGATCAAGTGGAAGGACGATTCTCCGTGATAGGCAGTGGAACACTGGATGTAGAGCTAGAAATAGCAAGTGAGCAG
ATCTAGAGGAAAGGACGAATCTCCGTGATAGGCAGTGGAACACTGGTATGAGAGCTAGAACTAGCAAGTTAATAGA
TCTTGAGGAAAGGACGAAACTCCGTGATAGGCAGTGGAACACTGGTTTTAGAGCTAGAAAGCGCAAGTTAAAAGAC
And the output should be File C:
2 GAGGACAGACTACTAAAGCC
4 CTTGCCGCAGATTATCAGAG
0 CCAGCTTGATGTGTCCTGTG
3 TGATAGGCAGTGGAACACTG
I would like to do this using grep and I've tried a few variations of -c,o,f but I can't seem to get the right output.
How can I achieve this?
Try this
for i in `cat a`; do echo "$i `grep $i -c b`"; done
In this case if line from file A occurred several times in one line of file B then this will be count as one occurrence. If you want to count such occurrences but without its overlapping use this
for i in `cat a`; do printf $i; grep $i -o b | wc -l; done
And maybe this variant would be quicker
cat b | grep "`cat a`" -o | sort | uniq -c
#!/usr/bin/perl
open A, "A"; # open file "A" to handle A
open B, "B"; # open file "B" to handle B
chomp(#keys = <A>); # read keys to array, strip line-feeds
#counts{#keys} = (0) x #keys; # initialize hash counts for keys
while(<B>){ # iterate file handle B line by line
foreach $k (#keys){ # iterate keys array
if (/$k/) { # if key matches line
$counts{$k}++; # increase count for key by one
}
}
}
print "$counts{$_} $_\n" for (keys %counts);
Linux command to compare files:
comm FileA FileB
comm produces three-column output. Column one contains lines unique to FileA, column two contains lines unique to FileB, and column three contains lines common to both files.
My file is as below
file name = test
1 abc
2 xyz
3 pqr
How can i convert second column of file in upper case without using awk or sed.
You can use tr to transform from lowercase to uppercase. cut will extract the single columns and paste will combine the separated columns again.
Assumption: Columns are delimited by tabs.
paste <(cut -f1 file) <(cut -f2 file | tr '[:lower:]' '[:upper:]')
Replace file with your file name (that is test in your case).
In pure bash
#!/bin/bash
while read -r col1 col2;
do
printf "%s%7s\n" "$col1" "${col2^^}"
done < file > output-file
Input-file
$ cat file
1 abc
2 xyz
3 pqr
Output-file
$ cat output-file
1 ABC
2 XYZ
3 PQR
This question already has an answer here:
Use awk to sum or average for each unique ID
(1 answer)
Closed 6 years ago.
I have a file that contains several comma-separated columns, including a customer ID in the first column.
One customer ID may occur on several rows, but always refers to the same real customer.
How do I run basic calculations in a shell script based on this ID column? For example, calculating the sum of the mileages (the 5th field) for the given customer ID.
102,305,Jin,Kerala,40
104,308,Paul,US,45
105,350,Nina,AUS,50
102,390,Jin,Kerala,10
104,395,Paul,US,35
102,399,Jin,Kerala,35
5th field is the mileage, 1st field is the customer ID.
This is a simple awk script that will sum up the mileages and print the customer IDs together with the sums at the end:
#!/usr/bin/awk -f
BEGIN { FS = "," }
{
customer_id = $1;
mileage = $5;
total_mileage[customer_id] += mileage;
}
END {
for (customer_id in total_mileage) {
print customer_id, total_mileage[customer_id];
}
}
To run (after making it executable with chmod +x script.awk):
$ ./script.awk data.in
102 85
104 80
105 50
Alternatively, as a "one-liner":
$ awk -F, '{t[$1]+=$5} END {for (c in t){print c,t[c]}}' data.in
102 85
104 80
105 50
While I agree with #wilx that using a database might be smarter, this sample awk script should get you started:
awk -v FS=',' '{miles[$1] += $5}
END { for (customerid in miles) {
print customerid, miles[customerid]; } }' customers
You can get a list of unique IDs using something like (assuming the first column is the ID):
awk '{print $1}' inputFile | sort -u
This outputs the first field of every single line in the input file inputFile, sorts them and removes duplicates.
You can then use that method with a bash loop to process each of the unique IDs with another awk command to perform some action on them. In the following snippet, I print out the matching lines for each ID:
for id in $(awk '{print $1}' inputFile | sort -u) ; do
echo "${id}:"
awk -vid=${id} '$1==id {print " "$0)' inputFile
done
In that code, for each individual ID, it first outputs the ID then uses awk to only process lines matching that ID. The action carried out is to output the full line with indentation.
Of course, you can do anything you wish with the lines matching each ID. As shown below, an example more closely matching your requirements.
First, here's an input file I used for testing - we can assume field 1 is the customer ID and field 2 the mileage:
$ cat inputFile
a 1
b 2
c 3
a 4
b 5
c 6
a 7
b 8
c 9
b 10
c 11
c 12
And here's a command-line transcript of the method proposed (note that $ and + are input prompt and continuation prompt respectively, they are not part of the actual commands):
$ for id in $(awk '{print $1}' inputFile | sort -u) ; do
+ awk -vid=${id} '
+ $1==id {print $0; sum += $2 }
+ END {print "Total: "sum; print }
+ ' inputFile
+ done
a 1
a 4
a 7
Total: 12
b 2
b 5
b 8
b 10
Total: 25
c 3
c 6
c 9
c 11
c 12
Total: 41
Keep in mind that, for non-huge data sets, it's also possible to do this in a single pass awk script, using associative arrays to store the totals then outputting all the data in the END block. I myself tend to prefer the multi-pass approach myself since it minimises the possibility of running out of memory. The trade-off, of course, is that it will no doubt take longer since you're processing the file more than once.
For a single-pass solution, you can use something like:
$ awk '{sum[$1] += $2} {for (key in sum) { print key": "sum[key]}}' inputFile
which gives you:
a: 12
b: 25
c: 41
How can I compare this 2 big files in unix.
I've already tried using 'grep -Fxvf file1.txt file2.txt | wc -l' but the output is 2,000,480 and when switching file1 and file2 the output is 1,999,999.
How can I get the output of '480' because that's what i am expecting.
I've also tried using diff/cmp commands but the output is too complicated.
I think you want an absolute value of a difference in line numbers in 2 files. You can achieve it easily with awk and get a decent result. You'd read numbers of lines in an array and later subtract the array values in the END block. For pure shell it'd have to get more complex. Imagine you get some test data generated (10 and 14 line files):
$ seq 1 10 > ten
$ seq 1 14 > fourteen
And then you do:
$ ( wc -l ten ; wc -l fourteen ) | awk '{ print $1}' | sort -rn | xargs -J % echo % - p | dc
The result:
4
But much better way would be do just do it in 3 lines (get word count for file1, then file2 and then subtract)